When I first got into marathoning, it was an offshoot of triathlon training, so needless to say I was biking and running a lot at the same time. After a long ride I was less tired than after a long run, so I always took my recuperate/cross training day after the long run. My recuperative day was really easy; some combination of a 1-2 mile jog, 2 miles of walking, leisurely bike ride, beer and wings, and/or weight training. I pretty much never did a run of any substance after a long run.
I also found that a quick transition from bike to running was best for me, so I would run immediately after biking (maybe you should trying running when you get home from work?). I would usually eat something during my ride (a cliff bar, pb & j sandwich, apple or something) so that I would have energy for the run to follow.
I liked Hal Higdon's training programs,
http://www.halhigdon.com/marathon/inter2.html
and have followed those during the several times I've done marathon training.